The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in Arabidopsis thaliana L. using resources GEO NCBI, string-db, ShinyGO, STREME, and Tomtom, as well as programs metaRE, CisCross, and Cytoscape. Through the meta-analysis of five transcriptomic experiments, we selected a set of 1151 differentially expressed genes, including 453 genes that compose the gene network. Ten significantly enriched regulatory motifs for TFs families ZF-HD, HB, C2H2, NAC, BZR, and ARID were found in the promoter regions of differentially expressed genes. In addition, we predicted families of transcription factors associated with the duration of exposure (RAV, HSF), intensity of high light treatment (MYB, REM), and the direction of gene expression change (HSF, S1Fa-like). We predicted genetic components systems involved in a high light response and their expression changes, potential transcriptional regulators, and associated processes.

The thraustochytrids are a group of marine protists known for their significant ecological roles as decomposers and parasites as well as for their potential biotechnological applications, yet their evolutionary and structural diversity remains poorly understood. Our review critically examines the phylogeny of this taxa, utilizing available up-to-date knowledge and their taxonomic classifications. Additionally, advanced imaging techniques, including electron microscopy, are employed to explore the ultrastructural characteristics of these organisms, revealing key features that contribute to their adaptive capabilities in varying marine environments. The integration of this knowledge with available omics data highlights the huge biotechnological potential of thraustochytrids, particularly in producing $\omega$-3 fatty acids and other bioactive compounds. Our review underscores the importance of a systems biology approach in understanding thraustochytrids biology and highlights the urgent need for novel, accurate omics research to unlock their full biotechnological potential. Overall, this review aims to foster a deeper appreciation of thraustochytrids by synthesizing information on their evolution, ultrastructure, and practical applications, thereby providing a foundation for future studies in microbiology and biotechnology.

The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.

For the first time, we used an in vitro vs. in vivo experimental design to reveal core pathways under nitrogen deficiency (ND) in an evergreen tree crop. These pathways were related to lignin biosynthesis, cell redox homeostasis, the defense response to fungus, the response to Karrikin, amino acid transmembrane transport, the extracellular region, the cellular protein catabolic process, and aspartic-type endopeptidase activity. In addition, the mitogen-activated protein kinase pathway and ATP synthase (ATP)-binding cassette transporters were significantly upregulated under nitrogen deficiency in vitro and in vivo. Most of the MAPK downstream genes were related to calcium signaling (818 genes) rather than hormone signaling (157 genes). Moreover, the hormone signaling pathway predominantly contained auxin- and abscisic acid-related genes, indicating the crucial role of these hormones in ND response. Overall, 45 transcription factors were upregulated in both experiments, 5 WRKYs, 3 NACs, 2 MYBs, 2 ERFs, HD-Zip, RLP12, bHLH25, RADIALIS-like, and others, suggesting their ND regulation is independent from the presence of a root system. Gene network reconstruction displayed that these transcription factors participate in response to fungus/chitin, suggesting that nitrogen response and pathogen response have common regulation. The upregulation of lignin biosynthesis genes, cytochrome genes, and strigalactone response genes was much more pronounced under in vitro ND as compared to in vivo ND. Several cell wall-related genes were closely associated with cytochromes, indicating their important role in flavanols biosynthesis in tea plant. These results clarify the signaling mechanisms and regulation of the response to nitrogen deficiency in evergreen tree crops.

The innate immune system (IIS) is an ancient and essential defense mechanism that protects animals against a wide range of pathogens and diseases. Although extensively studied in mammals, our understanding of the IIS in other taxa remains limited. The zebrafish (Danio rerio) serves as a promising model organism for investigating IIS-related processes, yet the immunogenetics of fish are not fully elucidated. To address this gap, we conducted a meta-analysis of single-cell RNA sequencing (scRNA-seq) datasets from zebrafish kidney marrow, encompassing approximately 250,000 immune cells. Our analysis confirms the presence of key genetic pathways in zebrafish innate immune cells that are similar to those identified in mammals. Zebrafish macrophages specifically express genes encoding cathepsins, major histocompatibility complex class II proteins, integral membrane proteins, and the V-ATPase complex and demonstrate the enrichment of oxidative phosphorylation ferroptosis processes. Neutrophils are characterized by the significant expression of genes encoding actins, cytoskeleton organizing proteins, the Arp2/3 complex, and glycolysis enzymes and have demonstrated their involvement in GnRH and CLR signaling pathways, adherents, and tight junctions. Both macrophages and neutrophils highly express genes of NOD-like receptors, phagosomes, and lysosome pathways and genes involved in apoptosis. Our findings reinforce the idea about the existence of a wide spectrum of immune cell phenotypes in fish since we found only a small number of cells with clear pro- or anti-inflammatory signatures.

Nowadays, with the accumulation of large amounts of stress-response transcriptomic data in plants, it is possible to clarify the key genes and transcription factors (TFs) involved in these processes. Here, we present the comprehensive transcriptomic meta-analysis of the high light (HL) response in photosynthetic tissues of Arabidopsis thaliana (L.) Heynh., offering new insights into adaptation mechanisms of plants to excessive light and involved gene regulatory networks. We analyzed 21 experiments covering 58 HL conditions in total, yielding 218,000 instances of differentially expressed genes (DEGs) corresponding to 19,000 unique genes. Based on these data, we developed the publicly accessible AraLightDEGs resource, which offers multiple search filters for experimental conditions and gene characteristics, and we conducted a detailed meta-analysis using our R pipeline, AraLightMeta. Our meta-analysis highlighted distinct transcriptional programs between short- and long-term HL responses in leaves, revealing novel regulatory interactions and refining the understanding of key DEGs. In particular, long-term HL adaptation involves key TFs such as CRF3 and PTF1 regulating antioxidant and jasmonate signaling; ATWHY2, WHY3, and emb2746 coordinating chloroplast and mitochondrial gene expression; AT2G28450 governing ribosome biogenesis; and AT4G12750 controlling methyltransferase activity. We integrated these findings into a conceptual scheme illustrating transcriptional regulation and signaling processes in leaf cells responding to long-term HL stress.